Inclusive model of expression dynamics with conventional or metabolic labeling based scRNA-seq / multiomics, vector field reconstruction and differential geometry analyses

CellRank: dynamics from multi-view single-cell data

A guide to using a Seurat object in conjunction with RNA Velocity

Predict RNA velocity through deep learning

Toolkit for Single-Cell Velocity

𝒫robabilistic modeling of RNA velocity ⬱

Dynamical systems methods for RNA velocity analysis

Inclusive and efficient quantification of labeling and splicing RNAs for time-resolved metabolic labeling based scRNA-seq experiments

Module 4 for HKU Single-cell Workshop

Simulation based inference of differentiation trajectories from RNA velocity fields.

Spatial Transcriptomics Quantification pipeline for 10x Visium and H&E-stained whole slide images

Tutorials for using BRIE

Characterize gene dynamics over trajectories using GLMs, GEEs, & GLMMs.

Entrain: Predicting Environmental Regulators of Differentiation Trajectories

R pacakge for RNA velocity estimation with nonlinear models

Dockerized Velocyto for RNA Velocity

Retinal ganglion cells regeneration in 2 days post optic nerve crush retina | Lydia Tai | Dong Feng Chen Lab collaboration | Schepens Eye Research Institute, Mass General Hospital, Harvard Medical School

IGFBPL1 Retinal Microglia Project | Dong Feng Chen Lab collaboration | Schepens Eye Research Institute, Mass General Hospital, Harvard Medical School

collab | DFC

This repository contains coding scripts utilized for the analysis of Longitudinal scRNAseq of human pancreatic slices datasets